scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data
Daniel Osorio, Yan Zhong, Guanxun Li, Jianhua Z. Huang, James J. Cai
Abstract
We present scTenifoldNet-a machine learning workflow built upon principal-component regression, low-rank tensor approximation, and manifold alignment-for constructing and comparing single-cell gene regulatory networks (scGRNs) using data from single-cell RNA sequencing. scTenifoldNet reveals regulatory changes in gene expression between samples by comparing the constructed scGRNs. With real data, scTenifoldNet identifies specific gene expression programs associated with different biological processes, providing critical insights into the underlying mechanism of regulatory networks governing cellular transcriptional activities.
Topics & Concepts
WorkflowComputational biologyGene regulatory networkTranscriptomeComputer scienceGene expressionRegulation of gene expressionGeneMechanism (biology)Principal component analysisRank (graph theory)Tensor (intrinsic definition)Data miningBiologyArtificial intelligenceMachine learningGeneticsMathematicsDatabaseEpistemologyPhilosophyPure mathematicsCombinatoricsSingle-cell and spatial transcriptomicsGenomics and Chromatin DynamicsGene Regulatory Network Analysis